rs11996715

Positions:

• chr8-140637192-C-A
• chr8-140637192-C-T

Variant summary

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

The XM_011516968.3(AGO2):​c.-117+5001G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,132 control chromosomes in the GnomAD database, including 14,739 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 0.42 (14738 hom., cov: 33)
  • Exomes 𝑓: 0.43 (1 hom.)
• Consequence: AGO2 XM_011516968.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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]

ERICD (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGO2	XM_011516968.3	c.-117+5001G>T		intron_variant			XP_011515270.3
ERICD	NR_170171.1	n.2958C>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERICD	ENST00000623655.2	n.912C>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64384 AN: 152000 Hom.: 14732 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.429 AC: 6 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.417 AC XY: 5 AN XY: 12

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.423 AC: 64408 AN: 152118 Hom.: 14738 Cov.: 33 AF XY: 0.424 AC XY: 31506 AN XY: 74366

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.486

Alfa AF: 0.471 Hom.: 7013

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11996715; hg19: chr8-141647291;