rs2854116

Positions:

• chr11-116829453-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;