X-116172342-G-T
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 (★★).
Frequency
Consequence
NM_000686.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGTR2 | ENST00000371906.5 | c.62G>T | p.Gly21Val | missense_variant | Exon 3 of 3 | 1 | NM_000686.5 | ENSP00000360973.4 | ||
AGTR2 | ENST00000681852.1 | c.62G>T | p.Gly21Val | missense_variant | Exon 2 of 2 | ENSP00000505750.1 | ||||
AGTR2 | ENST00000680409.1 | n.530G>T | non_coding_transcript_exon_variant | Exon 1 of 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 provided Uncertain:1Benign:2
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not specified Benign:3
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. -
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Intellectual disability, X-linked 88 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at