chr8-140625507-G-A

Position:

• chr8-140625507-G-A

Variant summary

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

The XM_017014159.2(LOC107986982):​c.-2083C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 151,926 control chromosomes in the GnomAD database, including 1,522 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 0.083 (1522 hom., cov: 33)
• Consequence: LOC107986982 XM_017014159.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986982	XM_017014159.2	c.-2083C>T		5_prime_UTR_variant	1/2
AGO2	NM_012154.5	c.22+9978C>T		intron_variant		ENST00000220592.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGO2	ENST00000220592.10	c.22+9978C>T		intron_variant		1	NM_012154.5	P1
AGO2	ENST00000519980.5	c.22+9978C>T		intron_variant		1
AGO2	ENST00000523609.5	c.22+9978C>T		intron_variant, NMD_transcript_variant		1
AGO2	ENST00000517293.5	n.62+9978C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0824 AC: 12511 AN: 151808 Hom.: 1515 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.0235

Gnomad FIN AF: 0.00739

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00166

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0826 AC: 12544 AN: 151926 Hom.: 1522 Cov.: 33 AF XY: 0.0805 AC XY: 5979 AN XY: 74268

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.0315

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.0235

Gnomad4 FIN AF: 0.00739

Gnomad4 NFE AF: 0.00166

Gnomad4 OTH AF: 0.0617

Alfa AF: 0.0214 Hom.: 62

Bravo AF: 0.0939

Asia WGS AF: 0.0710 AC: 246 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	1.9
DANN	Benign	0.21

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: rs6578126; hg19: chr8-141635606;