rs11228551

Positions:

• chr11-69187526-T-A

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 0.24 in 152,100 control chromosomes in the GnomAD database, including 4,845 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 0.24 (4845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

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 = 0.297 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: 0.240 AC: 36499 AN: 151982 Hom.: 4846 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.240 AC: 36511 AN: 152100 Hom.: 4845 Cov.: 32 AF XY: 0.235 AC XY: 17466 AN XY: 74366

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.0174

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.268

Alfa AF: 0.271 Hom.: 758

Bravo AF: 0.235

Asia WGS AF: 0.119 AC: 413 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	0.15
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11228551; hg19: chr11-68954994;