rs3864659

Variant names:

• chr8-140545763-A-C
• rs3864659
• NM_012154.5:c.1749-1460T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-140545763-A-C
• chr8-140545763-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012154.5(AGO2):​c.1749-1460T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,176 control chromosomes in the GnomAD database, including 2,314 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 0.16 (2314 hom., cov: 33)
• Consequence: AGO2 NM_012154.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGO2	NM_012154.5	c.1749-1460T>G		intron_variant	Intron 13 of 18	ENST00000220592.10	NP_036286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGO2	ENST00000220592.10	c.1749-1460T>G		intron_variant	Intron 13 of 18	1	NM_012154.5	ENSP00000220592.5
AGO2	ENST00000519980.5	c.1749-1460T>G		intron_variant	Intron 13 of 17	1		ENSP00000430176.1
AGO2	ENST00000523609.5	n.*1334-1460T>G		intron_variant	Intron 12 of 17	1		ENSP00000430164.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23785 AN: 152058 Hom.: 2306 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.133

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23808 AN: 152176 Hom.: 2314 Cov.: 33 AF XY: 0.153 AC XY: 11386 AN XY: 74384

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0416

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.132

Alfa AF: 0.119 Hom.: 1640

Bravo AF: 0.162

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.65

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

Other links and lift over

dbSNP: rs3864659; hg19: chr8-141555862;