rs11228553

Variant names:

• chr11-69192716-T-G
• rs11228553

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 0.248 in 152,240 control chromosomes in the GnomAD database, including 5,007 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 0.25 (5007 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• 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: 0.248 AC: 37678 AN: 152120 Hom.: 5003 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.248 AC: 37703 AN: 152240 Hom.: 5007 Cov.: 33 AF XY: 0.244 AC XY: 18186 AN XY: 74438

African (AFR) AF: 0.182 AC: 7567 AN: 41542

American (AMR) AF: 0.200 AC: 3066 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1194 AN: 5180

South Asian (SAS) AF: 0.129 AC: 623 AN: 4826

European-Finnish (FIN) AF: 0.281 AC: 2979 AN: 10596

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20444 AN: 68002

Other (OTH) AF: 0.275 AC: 580 AN: 2112

Alfa AF: 0.289 Hom.: 3804

Bravo AF: 0.242

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.6
DANN	Benign	0.74
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs11228553; hg19: chr11-68960184;