rs11228594

Variant names:

• chr11-69255620-G-A
• rs11228594

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 0.232 in 151,808 control chromosomes in the GnomAD database, including 4,084 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 0.23 (4084 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.232 AC: 35191 AN: 151690 Hom.: 4079 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.232 AC: 35210 AN: 151808 Hom.: 4084 Cov.: 31 AF XY: 0.234 AC XY: 17338 AN XY: 74188

African (AFR) AF: 0.191 AC: 7885 AN: 41360

American (AMR) AF: 0.238 AC: 3625 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3464

East Asian (EAS) AF: 0.230 AC: 1183 AN: 5142

South Asian (SAS) AF: 0.180 AC: 867 AN: 4806

European-Finnish (FIN) AF: 0.254 AC: 2677 AN: 10536

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17200 AN: 67944

Other (OTH) AF: 0.258 AC: 542 AN: 2100

Alfa AF: 0.247 Hom.: 4239

Bravo AF: 0.232

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.83
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs11228594; hg19: chr11-69023087;