rs11236909

Positions:

• chr11-76728024-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 0.268 in 152,038 control chromosomes in the GnomAD database, including 5,678 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 0.27 (5678 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40678 AN: 151920 Hom.: 5660 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.268 AC: 40752 AN: 152038 Hom.: 5678 Cov.: 31 AF XY: 0.266 AC XY: 19734 AN XY: 74306

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.297

Alfa AF: 0.264 Hom.: 949

Bravo AF: 0.273

Asia WGS AF: 0.180 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	13
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11236909; hg19: chr11-76439068;