1-35888584-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_012199.5(AGO1):c.183G>A(p.Pro61Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000792 in 1,614,128 control chromosomes in the GnomAD database, including 19 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. P61P) has been classified as Benign.
Frequency
Consequence
NM_012199.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGO1 | NM_012199.5 | c.183G>A | p.Pro61Pro | synonymous_variant | Exon 2 of 19 | ENST00000373204.6 | NP_036331.1 | |
AGO1 | NM_001317122.2 | c.183G>A | p.Pro61Pro | synonymous_variant | Exon 2 of 19 | NP_001304051.1 | ||
AGO1 | XM_011541236.3 | c.183G>A | p.Pro61Pro | synonymous_variant | Exon 2 of 19 | XP_011539538.1 | ||
AGO1 | NM_001317123.2 | c.-43G>A | 5_prime_UTR_variant | Exon 2 of 19 | NP_001304052.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00128 AC: 194AN: 152150Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00305 AC: 767AN: 251316Hom.: 17 AF XY: 0.00236 AC XY: 320AN XY: 135828
GnomAD4 exome AF: 0.000742 AC: 1084AN: 1461860Hom.: 17 Cov.: 31 AF XY: 0.000637 AC XY: 463AN XY: 727230
GnomAD4 genome AF: 0.00127 AC: 194AN: 152268Hom.: 2 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
AGO1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 06, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at