Variant 1-36069043-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024852.4(AGO3):c.*13298G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,168 control chromosomes in the GnomAD database, including 43,481 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 0.72 ( 43476 hom., cov: 32)

Exomes 𝑓: 0.81 ( 5 hom. )

Consequence

AGO3
NM_024852.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.762

Variant links:

Genes affected

AGO3 (HGNC:18421): (argonaute RISC catalytic component 3) This gene encodes a member of the Argonaute family of proteins which play a role in RNA interference. The encoded protein is highly basic, contains a PAZ domain and a PIWI domain, and may play a role in short-interfering-RNA-mediated gene silencing. This gene is located on chromosome 1 in a tandem cluster of closely related family members including argonaute 4 and eukaryotic translation initiation factor 2C, 1. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

AGO3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGO3	NM_024852.4 linkuse as main transcript	c.*13298G>T		3_prime_UTR_variant	19/19	ENST00000373191.9	NP_079128.2	Q9H9G7-1B4E1P5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGO3	ENST00000373191.9 linkuse as main transcript	c.*13298G>T		3_prime_UTR_variant	19/19	2	NM_024852.4	ENSP00000362287.3		Q9H9G7-1

Frequencies

GnomAD3 genomes

AF:

0.723

AC:

109943

AN:

152034

Hom.:

43484

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.961

Gnomad AMR

AF:

0.665

Gnomad ASJ

AF:

0.864

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.841

Gnomad FIN

AF:

0.821

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.910

Gnomad OTH

AF:

0.755

GnomAD4 exome

AF:

0.813

AC:

AN:

Hom.:

Cov.:

AF XY:

0.800

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.917

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.723

AC:

109958

AN:

152152

Hom.:

43476

Cov.:

AF XY:

0.717

AC XY:

53361

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.428

Gnomad4 AMR

AF:

0.664

Gnomad4 ASJ

AF:

0.864

Gnomad4 EAS

AF:

0.319

Gnomad4 SAS

AF:

0.840

Gnomad4 FIN

AF:

0.821

Gnomad4 NFE

AF:

0.910

Gnomad4 OTH

AF:

0.755

Alfa

AF:

0.852

Hom.:

30973

Bravo

AF:

0.691

Asia WGS

AF:

0.619

AC:

2153

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.5

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over