rs11221522

Positions:

• chr11-128946326-G-A
• chr11-128946326-G-C

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 0.179 in 152,040 control chromosomes in the GnomAD database, including 2,629 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 0.18 (2629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.179 AC: 27242 AN: 151922 Hom.: 2633 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.179 AC: 27244 AN: 152040 Hom.: 2629 Cov.: 33 AF XY: 0.180 AC XY: 13399 AN XY: 74328

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.146

Alfa AF: 0.202 Hom.: 402

Bravo AF: 0.164

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
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: rs11221522; hg19: chr11-128816221;