rs2854116

Variant names:

• chr11-116829453-C-T
• rs2854116

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 0.518 in 151,934 control chromosomes in the GnomAD database, including 21,877 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 0.52 (21877 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78625 AN: 151818 Hom.: 21882 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.518 AC: 78649 AN: 151934 Hom.: 21877 Cov.: 33 AF XY: 0.512 AC XY: 38039 AN XY: 74234

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.534

Alfa AF: 0.548 Hom.: 4592

Bravo AF: 0.516

Asia WGS AF: 0.487 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2854116; hg19: chr11-116700169;