rs4762
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000366667.6(AGT):c.593C>T(p.Thr198Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 1,613,596 control chromosomes in the GnomAD database, including 12,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T198T) has been classified as Likely benign.
Frequency
Consequence
ENST00000366667.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGT | NM_001384479.1 | c.593C>T | p.Thr198Met | missense_variant | 2/5 | ENST00000366667.6 | NP_001371408.1 | |
AGT | NM_001382817.3 | c.593C>T | p.Thr198Met | missense_variant | 2/5 | NP_001369746.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGT | ENST00000366667.6 | c.593C>T | p.Thr198Met | missense_variant | 2/5 | 1 | NM_001384479.1 | ENSP00000355627 | P1 |
Frequencies
GnomAD3 genomes AF: 0.112 AC: 17040AN: 152154Hom.: 1082 Cov.: 33
GnomAD3 exomes AF: 0.124 AC: 31006AN: 249646Hom.: 2077 AF XY: 0.124 AC XY: 16806AN XY: 135222
GnomAD4 exome AF: 0.123 AC: 179076AN: 1461324Hom.: 11353 Cov.: 38 AF XY: 0.123 AC XY: 89491AN XY: 726958
GnomAD4 genome AF: 0.112 AC: 17033AN: 152272Hom.: 1080 Cov.: 33 AF XY: 0.115 AC XY: 8532AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | This variant is associated with the following publications: (PMID: 25966146, 1394429, 20702504, 17145981, 20854100) - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Renal tubular dysgenesis Benign:1
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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at