11-2116909-A-G

Position:

• chr11-2116909-A-G

Variant summary

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

The variant allele was found at a frequency of 0.715 in 152,130 control chromosomes in the GnomAD database, including 39,110 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 0.71 (39110 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2116909A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108618 AN: 152012 Hom.: 39065 Cov.: 33

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.715 AC: 108724 AN: 152130 Hom.: 39110 Cov.: 33 AF XY: 0.711 AC XY: 52883 AN XY: 74346

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.704

Alfa AF: 0.709 Hom.: 23552

Bravo AF: 0.722

Asia WGS AF: 0.534 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6578985; hg19: chr11-2138139;