1-230710048-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001384479.1(AGT):āc.776T>Cā(p.Met259Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,613,874 control chromosomes in the GnomAD database, including 191,182 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001384479.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGT | NM_001384479.1 | c.776T>C | p.Met259Thr | missense_variant | 2/5 | ENST00000366667.6 | |
AGT | NM_001382817.3 | c.776T>C | p.Met259Thr | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGT | ENST00000366667.6 | c.776T>C | p.Met259Thr | missense_variant | 2/5 | 1 | NM_001384479.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.578 AC: 87869AN: 152062Hom.: 27970 Cov.: 33
GnomAD3 exomes AF: 0.548 AC: 137772AN: 251344Hom.: 41270 AF XY: 0.536 AC XY: 72890AN XY: 135888
GnomAD4 exome AF: 0.458 AC: 669469AN: 1461692Hom.: 163148 Cov.: 65 AF XY: 0.462 AC XY: 335636AN XY: 727170
GnomAD4 genome AF: 0.578 AC: 87993AN: 152182Hom.: 28034 Cov.: 33 AF XY: 0.583 AC XY: 43390AN XY: 74390
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Renal tubular dysgenesis Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This 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:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 13, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Hypertensive disorder Benign:1
Benign, no assertion criteria provided | reference population | iDNA Genomics | Oct 12, 2021 | - - |
Preeclampsia, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jan 01, 2005 | - - |
Hypertension, essential, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jan 01, 2005 | - - |
Susceptibility to progression to renal failure in IgA nephropathy Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jan 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at