rs121917810
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_000686.5(AGTR2):c.62G>T(p.Gly21Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00403 in 1,208,856 control chromosomes in the GnomAD database, including 13 homozygotes. There are 1,581 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G21R) has been classified as Uncertain significance.
Frequency
Consequence
NM_000686.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGTR2 | NM_000686.5 | c.62G>T | p.Gly21Val | missense_variant | 3/3 | ENST00000371906.5 | |
AGTR2 | NM_001385624.1 | c.62G>T | p.Gly21Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTR2 | ENST00000371906.5 | c.62G>T | p.Gly21Val | missense_variant | 3/3 | 1 | NM_000686.5 | P1 | |
AGTR2 | ENST00000681852.1 | c.62G>T | p.Gly21Val | missense_variant | 2/2 | P1 | |||
AGTR2 | ENST00000680409.1 | n.530G>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00273 AC: 304AN: 111214Hom.: 2 Cov.: 23 AF XY: 0.00233 AC XY: 78AN XY: 33490
GnomAD3 exomes AF: 0.00251 AC: 459AN: 183135Hom.: 4 AF XY: 0.00253 AC XY: 171AN XY: 67693
GnomAD4 exome AF: 0.00417 AC: 4576AN: 1097590Hom.: 11 Cov.: 31 AF XY: 0.00414 AC XY: 1505AN XY: 363134
GnomAD4 genome ? AF: 0.00271 AC: 301AN: 111266Hom.: 2 Cov.: 23 AF XY: 0.00227 AC XY: 76AN XY: 33552
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 15, 2013 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2015 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Aug 08, 2013 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Intellectual disability, X-linked 88 Benign:1
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at