rs7834784
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_017014159.2(LOC107986982):c.*7869A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,048 control chromosomes in the GnomAD database, including 8,790 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.33 ( 8790 hom., cov: 32)
Consequence
LOC107986982
XM_017014159.2 3_prime_UTR
XM_017014159.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.443
Genes affected
AGO2 (HGNC:3263): (argonaute RISC catalytic component 2) This gene encodes a member of the Argonaute family of proteins which play a role in RNA interference. The encoded protein is highly basic, and contains a PAZ domain and a PIWI domain. It may interact with dicer1 and play a role in short-interfering-RNA-mediated gene silencing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC107986982 | XM_017014159.2 | c.*7869A>G | 3_prime_UTR_variant | 2/2 | |||
AGO2 | NM_012154.5 | c.22+21105A>G | intron_variant | ENST00000220592.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGO2 | ENST00000220592.10 | c.22+21105A>G | intron_variant | 1 | NM_012154.5 | P1 | |||
AGO2 | ENST00000519980.5 | c.22+21105A>G | intron_variant | 1 | |||||
AGO2 | ENST00000523609.5 | c.22+21105A>G | intron_variant, NMD_transcript_variant | 1 | |||||
AGO2 | ENST00000517293.5 | n.62+21105A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.334 AC: 50778AN: 151930Hom.: 8778 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.334 AC: 50817AN: 152048Hom.: 8790 Cov.: 32 AF XY: 0.332 AC XY: 24696AN XY: 74354
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821
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at