rs11228565

Variant names:

• chr11-69211113-G-A
• rs11228565

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 0.162 in 152,222 control chromosomes in the GnomAD database, including 2,269 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 0.16 (2269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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: 0.162 AC: 24702 AN: 152104 Hom.: 2270 Cov.: 32

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.162 AC: 24687 AN: 152222 Hom.: 2269 Cov.: 32 AF XY: 0.161 AC XY: 11956 AN XY: 74420

Gnomad4 AFR AF: 0.0923

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.0495

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.191

Alfa AF: 0.203 Hom.: 5277

Bravo AF: 0.158

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11228565; hg19: chr11-68978580;