rs11236909

Variant names:

• chr11-76728024-A-G
• rs11236909

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.326 AC: 13538 AN: 41474

American (AMR) AF: 0.246 AC: 3759 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1054 AN: 5138

South Asian (SAS) AF: 0.191 AC: 916 AN: 4808

European-Finnish (FIN) AF: 0.197 AC: 2085 AN: 10570

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16764 AN: 67978

Other (OTH) AF: 0.297 AC: 627 AN: 2112

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
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs11236909; hg19: chr11-76439068;