chr11-116746524-A-C

Position:

• chr11-116746524-A-C

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/exons	MANE	UniProt

Ensembl

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