rs11228563

Positions:

• chr11-69209529-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 0.262 in 151,992 control chromosomes in the GnomAD database, including 5,594 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 0.26 (5594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.262 AC: 39797 AN: 151874 Hom.: 5587 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.262 AC: 39831 AN: 151992 Hom.: 5594 Cov.: 32 AF XY: 0.259 AC XY: 19272 AN XY: 74284

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.0138

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.281

Alfa AF: 0.291 Hom.: 9473

Bravo AF: 0.258

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.031
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11228563; hg19: chr11-68976996;