chr1-230710048-A-C

Variant names:

• chr1-230710048-A-C
• rs699
• NM_001384479.1:c.776T>G
• AGT p.Met259Arg

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

0 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 0 classification points (ACMG Germline Pathogenicity v2019). PM2BP4_Moderate

The NM_001384479.1(AGT):c.776T>G (p.Met259Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.M259T: Benign (ClinVar VariationId 18068, 2 stars)

• Frequency: Genomes: not found (cov: 33)
• Consequence: AGT NM_001384479.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 1096 publications found

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]

AGT Gene-Disease associations (from GenCC):

• renal tubular dysgenesis of genetic origin

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 0 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: AR) (threshold 0.001) — PM2 moderate.
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Moderate).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_001384479.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	AGT NM_001384479.1	MANE Select	c.776T>G p.Met259Arg	missense	Exon 2 of 5	Prot: NP_001371408.1 UniProt:
	AGT NM_001382817.3		c.776T>G p.Met259Arg	missense	Exon 2 of 5	Prot: NP_001369746.2 UniProt:

AGT NM_001384479.1

MANE Select

HGVSc / HGVSpc.776T>Gp.Met259Arg

Exon rankExon 2 of 5

missense

Prot: NP_001371408.1UniProt: P01019A0A7P0T8D1

AGT NM_001382817.3

HGVSc / HGVSpc.776T>Gp.Met259Arg

Exon rankExon 2 of 5

missense

Prot: NP_001369746.2UniProt: P01019A0A7P0T8D1

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	AGT ENST00000366667.6	TSL:1MANE Select	c.776T>G p.Met259Arg	missense	Exon 2 of 5	Prot: ENSP00000355627.5 UniProt:
	AGT ENST00000680041.1		c.776T>G p.Met259Arg	missense	Exon 2 of 5	Prot: ENSP00000504866.1 UniProt:
	AGT ENST00000681269.1		c.776T>G p.Met259Arg	missense	Exon 2 of 5	Prot: ENSP00000505985.1 UniProt:

AGT ENST00000366667.6

TSL:1MANE Select

HGVSc / HGVSpc.776T>Gp.Met259Arg

Exon rankExon 2 of 5

missense

Prot: ENSP00000355627.5UniProt: P01019

AGT ENST00000680041.1

HGVSc / HGVSpc.776T>Gp.Met259Arg

Exon rankExon 2 of 5

missense

Prot: ENSP00000504866.1UniProt: P01019

AGT ENST00000681269.1

HGVSc / HGVSpc.776T>Gp.Met259Arg

Exon rankExon 2 of 5

missense

Prot: ENSP00000505985.1UniProt: P01019

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:65
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	6.4
AlphaMissense	Benign	0.055
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	2.5
DANN	Benign	0.44
DEOGEN2	Benign	0.21	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.066	N
FuncVEP CTI	Benign	0.0099
GPN-Star LLR	N/A	0.41
GPN-Star score	N/A	-0.41
LIST_S2	Benign	0.13	T
M_CAP	Benign	0.070	D
MetaRNN	Benign	0.073	T
MetaSVM	Benign	-0.84	T
Mutation Taster	N/A	98/2	polymorphism
MutationAssessor	Benign	0.0	N
PhyloP100	Benign	0.51
popEVE	Benign	-2.6
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.050	N
RBP_binding_hub_radar	N/A	0.0
RBP_regulation_power_radar	N/A	1.1
REVEL	Benign	0.16
Sift	Benign	0.26	T
Sift4G	Benign	0.22	T
Varity_R	N/A	0.33
VESM-3B	Benign	-2.7

Showing 30 of 30 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs699;

hg19: chr1-230845794;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar