rs11228551

Variant names:

• chr11-69187526-T-A
• rs11228551

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 0.24 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.187 AC: 7742 AN: 41468

American (AMR) AF: 0.196 AC: 2998 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3468

East Asian (EAS) AF: 0.0174 AC: 90 AN: 5178

South Asian (SAS) AF: 0.107 AC: 518 AN: 4830

European-Finnish (FIN) AF: 0.280 AC: 2962 AN: 10568

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20395 AN: 67988

Other (OTH) AF: 0.268 AC: 566 AN: 2114

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs11228551; hg19: chr11-68954994;