rs11786030

chr8-140620073-G-Achr8-140620073-G-Cchr8-140620073-G-T

Variant summary

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

The XM_017014159.2(LOC107986982):c.*2176C>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 0.826 in 152,120 control chromosomes in the GnomAD database, including 52,233 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 0.83 (52233 hom., cov: 32)
• Consequence: LOC107986982 XM_017014159.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

Genes affected

LOC107986982 (HGNC:):

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986982	XM_017014159.2	c.*2176C>T		3_prime_UTR_variant	2/2
AGO2	NM_012154.5	c.22+15412C>T		intron_variant		ENST00000220592.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGO2	ENST00000220592.10	c.22+15412C>T		intron_variant		1	NM_012154.5	P1
AGO2	ENST00000519980.5	c.22+15412C>T		intron_variant		1
AGO2	ENST00000523609.5	c.22+15412C>T		intron_variant, NMD_transcript_variant		1
AGO2	ENST00000517293.5	n.62+15412C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125499 AN: 152000 Hom.: 52174 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.826 AC: 125616 AN: 152120 Hom.: 52233 Cov.: 32 AF XY: 0.821 AC XY: 61059 AN XY: 74352

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.848

Alfa AF: 0.837 Hom.: 70697

Bravo AF: 0.835

Asia WGS AF: 0.705 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.42
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: rs11786030; hg19: chr8-141630172;