rs11216126

Variant names:

• chr11-116746524-A-C
• rs11216126

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 0.116 in 152,248 control chromosomes in the GnomAD database, including 1,348 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 0.12 (1348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 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: 0.116 AC: 17657 AN: 152130 Hom.: 1347 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.116 AC: 17665 AN: 152248 Hom.: 1348 Cov.: 32 AF XY: 0.122 AC XY: 9117 AN XY: 74442

Gnomad4 AFR AF: 0.0456

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.104

Alfa AF: 0.126 Hom.: 2028

Bravo AF: 0.107

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11216126; hg19: chr11-116617240;